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1,000 results • Page
1 of 20
Sort: Rank
Rank
Views
Votes
Replies
0
votes
0
replies
12
views
Repeat CT in overrepresented sequences
ScRNA
fastqc
overrepresented
sequences
1 hour ago by
Analeigh
• 0
0
votes
0
replies
26
views
How to find the adapter sequence of an RNAseq dataset?
fastQC
trimming
adapter
RNAseq
2 hours ago by
Maryam
• 0
0
votes
1
reply
131
views
Can a read be aligned more than once?
alignment
gaf
read
sam
updated 11 hours ago by
GenoMax
146k • written 12 hours ago by
guntul
▴ 40
0
votes
0
replies
102
views
Is it possible to use multinichenet to find the targets of specific ligands coming from a specified cell type
multinicheNet
CCI
19 hours ago by
teofoskol
• 0
0
votes
2
replies
157
views
What to do with sequences without hits after doing blast against a reference transcriptome
without
hits
transcriptome
blast
updated 1 day ago by
Bastien Hervé
5.8k • written 1 day ago by
Biodee
• 0
0
votes
0
replies
93
views
why I get "Running twoBitToFa failed" when loading chopchop
CRISPR
command
line
twoBitToFa
chopchop
1 day ago by
WYZ1120zzh
• 0
0
votes
0
replies
116
views
TCGA differential DNA methylation analysis 450K best practices
methylation
HM450K
differential
1 day ago by
Brassicka
• 0
0
votes
3
replies
228
views
Conversion from .lib to .faa file
Conversion
FASTA
BLAST
updated 1 day ago by
GenoMax
146k • written 1 day ago by
watermicrogirl
• 0
0
votes
2
replies
237
views
Inquiry about depth of coverage and copy number variation
number
copy
CNV
sequencing
depth
variation
10 hours ago by
Chen
• 0
1
vote
1
reply
130
views
Finding Differential Phosphosites in TMT Phosphoproteomics Data
DEqMS
Mass
Phosphoproteomics
Proteomics
Spec
updated 1 day ago by
ATpoint
85k • written 1 day ago by
jesswhitts
• 0
0
votes
0
replies
95
views
Magnesium ion in a post-docking adjustment
Docking
Magnesium
Ion
1 day ago by
Rodolfo Adrián
• 0
0
votes
2
replies
177
views
R encountering fatal error and quitting the session
R
randomForestSRC
Random-forest
16 hours ago by
anjalivasudevan98
▴ 40
0
votes
0
replies
93
views
GWAS from direct samples... is imputation necessary?
imputation
PLINK
GWAS
1 day ago by
sabrilo171
▴ 10
2
votes
5
replies
374
views
GATK - Output differences in Calls when Split by chromosome intervals and without splitting
GATK
PICARD
MergeVcf
vcftools
1 day ago by
Maverick
▴ 10
0
votes
0
replies
95
views
mageck mle design matrix
crispr
mageck-mle
design-matrix
pooled-screen
1 day ago by
Assa Yeroslaviz
★ 1.9k
0
votes
2
replies
340
views
After subsetting a seurat object number of variable features is wrong.
FindVariableFeatures
seurat
subset
updated 1 day ago by
Ram
44k • written 10 weeks ago by
Assa Yeroslaviz
★ 1.9k
0
votes
0
replies
95
views
PyDeseq2 - InvalidIndexError
python
rna-seq
pandas
pydeseq2
deseq2
1 day ago by
tmanjonas
• 0
0
votes
0
replies
100
views
Finding the IC50 from GraphPad Prism
IC50
1 day ago by
camiinnocente
• 0
0
votes
0
replies
88
views
Pipelines for CAZenzymes, COG, KO, MetaCyc, Pfam and TIGRFAM analysis
PICRUSt2
Metagenomic
MicFunPred
updated 1 day ago by
Ram
44k • written 1 day ago by
Petrônio
• 0
0
votes
1
reply
151
views
Gene performance/coverage calculation methodology in .bam files using samtools
samtools
ngs
coverage
updated 1 day ago by
Ram
44k • written 1 day ago by
slzr_
• 0
0
votes
0
replies
90
views
(vg rna) some transcripts have multiple projections on haplotypes and abnormal length growth
vg
1 day ago by
Wenhai
• 0
1
vote
2
replies
185
views
De novo assembly with more genome size than expected
illumina
sequencing
assembly
genomics
updated 1 day ago by
GenoMax
146k • written 1 day ago by
Isidro
• 0
1
vote
0
replies
116
views
Enironmental metabolic ability - metagenomic assembly or MAGs
MAGs
environmental
microbiology
metagenomes
updated 1 day ago by
GenoMax
146k • written 1 day ago by
sipeskm
▴ 10
1
vote
0
replies
105
views
Stable coordinates in gaf files?
gfa
gaf
rgfa
1 day ago by
Uveyik
▴ 40
1
vote
2
replies
169
views
Dealing with outliers for differential expression in proteomics
proteomics
PCA
DEA
outliers
limma
updated 2 days ago by
ATpoint
85k • written 2 days ago by
Jorge HB
• 0
0
votes
1
reply
183
views
Differential expression genes(downstream analysis)
Bulk-RNAseq
updated 2 days ago by
pinheirofabiano
▴ 90 • written 2 days ago by
odi
▴ 10
0
votes
0
replies
112
views
How do I set the RNAhybrid parameters to get more accurate and as many results as possible
RNAhybrid
miRNA_target_genes_prediction
2 days ago by
bingyanzheng18
• 0
0
votes
0
replies
113
views
CIBERSORTx error (error in rep(2, size * length(cells) -1)) : invalid 'times' argument
CIBERSORTx
CIBERSORT
scRNA-seq
RNA-seq
Deconvolution
2 days ago by
Amairani
• 0
0
votes
2
replies
189
views
Reconciling old crystallography papers with modern sequencing data
PDB
proteomics
updated 19 hours ago by
Wayne
★ 2.1k • written 2 days ago by
John Ma
▴ 310
0
votes
0
replies
120
views
Evaluate homopolymeric tracts in a set of microbial genomes
genomes
genomics
updated 2 days ago by
Ram
44k • written 2 days ago by
Madde
▴ 10
0
votes
5
replies
259
views
Coverage/depth of merged bam files
samtools
updated 1 day ago by
GenoMax
146k • written 2 days ago by
slzr_
• 0
0
votes
1
reply
138
views
Multiple Synteny Plot using MCScanX.
Synteny
MCScanX
updated 2 days ago by
alex.zaccaron
▴ 470 • written 2 days ago by
a.bibek52
▴ 10
1
vote
5
replies
291
views
Distinguishing gfa and rgfa files
gfa
rgfa
updated 1 day ago by
GenoMax
146k • written 2 days ago by
guntul
▴ 40
1
vote
4
replies
232
views
Help with Generating Clustered Heatmap from Large Datasets
Heatmap
updated 2 days ago by
Mensur Dlakic
★ 28k • written 2 days ago by
ArtiCore
• 0
0
votes
1
reply
151
views
Pangenome analysis
roary
pangenome
bakta
prokka
updated 2 days ago by
Madde
▴ 10 • written 2 days ago by
erindarruci16
• 0
0
votes
0
replies
96
views
Discripancy in miRDeep2.pl and quantifier.pl outputs
miRDeep2
2 days ago by
otieno43
▴ 30
0
votes
0
replies
92
views
Alternative to BLAST with N and mismatches as input
BLAST
2 days ago by
gernophil
▴ 90
0
votes
0
replies
149
views
Best Practices for Handling Negative Values in MFI Data after log base 2 transformation with median normalization
normalization
statistics
log-transformation
updated 2 days ago by
Ram
44k • written 2 days ago by
Alaa Elsaghir
• 0
0
votes
1
reply
113
views
How to Process PacBio RS FASTQ Files from SRA for Genome Coassembly with Illumina Reads?
coassembly
fastq
pacbio
updated 2 days ago by
GenoMax
146k • written 2 days ago by
till
• 0
0
votes
2
replies
169
views
xCell output and immune cell ratio
statistics
immunedeconv
xCell
20 hours ago by
a.stef.44
▴ 10
0
votes
1
reply
126
views
Spades Genome Assembly
genome
spades
assembly
updated 2 days ago by
dthorbur
★ 2.5k • written 3 days ago by
Umer
▴ 120
0
votes
2
replies
136
views
Error in Trinity installation
Trinity
updated 2 days ago by
Ram
44k • written 3 days ago by
ongchip
• 0
0
votes
0
replies
103
views
How to normalize gene abundance from long read metagenomic data?
normalization
metagenomics
long-read
gene-abundance
3 days ago by
Adrián
• 0
0
votes
0
replies
105
views
SILVA vs PR2 vs both for 18S metabarcoding?
taxonomy
18S
metabarcoding
3 days ago by
hjarnek
▴ 20
0
votes
0
replies
121
views
Your suggestion how to annotate cell type from visium data
spatial-transcriptomics
3 days ago by
Chris
▴ 340
0
votes
0
replies
93
views
HAPMIX : interpretation of the 16 probabilities generated when run in DIPLOID mode
hapmix
3 days ago by
cshreya
• 0
0
votes
0
replies
100
views
Determing the effect of directionality on gene fusions
fusions
star-fusion
3 days ago by
Ben
▴ 20
0
votes
0
replies
116
views
Seeking Guidance on WGBS Analysis for F1-Hybrid Mapping
Methylation
Bismark
WGBS
Mapping
Hybrid
3 days ago by
binaryCode
▴ 10
1
vote
1
reply
165
views
What's going on with Ensembl?
biomaRt
ensembl
updated 3 days ago by
GenoMax
146k • written 3 days ago by
yura.grabovska
▴ 600
0
votes
0
replies
103
views
Mapping problem with bowtie2 paremeter --very-sensitive and --very-sensitive-local
mapping
soil
microbiome
metagenomic
4 days ago by
hophuquy0944
• 0
1,000 results • Page
1 of 20
Recent Votes
Comment: Finding Differential Phosphosites in TMT Phosphoproteomics Data
Answer: Compare Two Sigle-cell Sample for Differentially Expressed Genes (DEGs). How?
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Recent Replies
Answer: Compare Two Sigle-cell Sample for Differentially Expressed Genes (DEGs). How?
by
ATpoint
85k
> But How could I know if the difference comes from sample instead of sequencing runs or cohort-driven batch effect? You cannot. It's pe…
Comment: Comparing GSEA mutant data to wild type
by
conmul
• 0
Sorry that it was unclear in the post. The data is all CRISPR gene effect scores from DepMap. The 'significant genes' as mentioned in the p…
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by
king
• 0
Thank you for your answer, it's very inspiring.
Comment: Inquiry about depth of coverage and copy number variation
by
Chen
• 0
Thanks Pierre, I was actually thinking about the duplicate PCR reads and didn't explain it properly. I have found a post mentioning that qu…
Comment: Can a read be aligned more than once?
by
GenoMax
146k
Yes a read can be aligned more than once (I don't specifically know about gam/gaf). It would be called a "multi-mapping" read. You could im…
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by
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• 0
The choice of test depends on the types of variables involved and the hypothesis you have. But most importantly on the question you want am…
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I'd consider making a [block annotation](https://jokergoo.github.io/ComplexHeatmap-reference/book/heatmap-annotations.html#block-annotation…
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What do you mean by "significant gene"? How did you perform GSEA and on how did you rank your genes for it? From guesswork I might initiall…
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The DESeq2 manual tells us that the object class of vst() output is a subclass of RangedSummarizedExperiment. I suspect the methods applica…
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Did you perform blockwise module detection by any chance? Are your results object's contents sorted in blocks?
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The WGCNA implementation by Langfelder and Horvath provides various correlation methods to create the initial correlation matrix. I don't t…
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any idea, how can I display the labels Pre and POst on the top of the heatmap? I am looking at complexheatmap package as to how they displa…
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What p-value do you mean? When and how did you calculate it?
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What about some of the well known enhancer regions, the globin locus LCR? Likely to be highly sequenceable, and yet not on exome panels.
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One of the improvements that the using the `salmon` -> `tximport` -> `DESeq2` pipeline, over just a `counts`->`DESeq2` pipeline is the abil…
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